Analyze substrate solvation

This notebook demonstrates deposition of an SDS adsorption layer on a non-spherical AFM tip model.

Initialization

IPython magic

In [1]:
%load_ext autoreload
%autoreload 2
In [14]:
%aimport
Modules to reload:
all-except-skipped

Modules to skip:

Imports

In [2]:
import ase.io # here used for reading pdb files
from ase.visualize import view
from ase.visualize.plot import plot_atoms # has nasty offset issues
from cycler import cycler # here used for cycling through colors in plots
import datetime
import fabric # for pythonic ssh connections
from fireworks import LaunchPad, Firework, Tracker, Workflow 
from fireworks import FileTransferTask, PyTask, ScriptTask

# FireWorks functionality 
from fireworks import Firework, LaunchPad, ScriptTask, Workflow
from fireworks.user_objects.firetasks.templatewriter_task import TemplateWriterTask
from fireworks.user_objects.firetasks.filepad_tasks import AddFilesTask, GetFilesTask, GetFilesByQueryTask
from imteksimfw.fireworks.user_objects.firetasks.cmd_tasks import CmdTask
from fireworks.utilities.filepad import FilePad # direct FilePad access, similar to the familiar LaunchPad

from collections.abc import Iterable
import glob
import gc # manually clean up memory with gc.collect()
import gromacs # GromacsWrapper, here used for evoking gmc commands, reading and writing .ndx files
# from io import StringIO, TextIOWrapper
import io
from IPython.display import display, Image #, Video # display image files within notebook
from ipywidgets import Video  # display video within notebook
import itertools # for products of iterables
import json # generic serialization of lists and dicts
import jinja2 # here used for filling packmol input script template
import jinja2.meta # for gathering variables in a jinja2 template
import logging 
import matplotlib.pyplot as plt
import MDAnalysis as mda # here used for reading and analyzing gromacs trajectories
import MDAnalysis.analysis.rdf as mda_rdf
import MDAnalysis.analysis.rms as mda_rms
from mpl_toolkits.mplot3d import Axes3D # here used for 3d point cloud scatter plot
import miniball # finds minimum bounding sphere of a point set
import nglview
import numpy as np
import os, os.path
import pandas as pd
import panedr # reads GROMACS edr into pandas df, requires pandas and pbr
import parmed as pmd # has quite a few advantages over ASE when it comes to parsing pdb
from pprint import pprint
import pymongo # for sorting in queries
import scipy.constants as sc
import subprocess # used for evoking external packmol
import sys
import tempfile
import yaml
NOTE: Some configuration directories are not set up yet: 
	/home/centos/.gromacswrapper
	/home/centos/.gromacswrapper/qscripts
	/home/centos/.gromacswrapper/templates
NOTE: You can create the configuration file and directories with:
	>>> import gromacs
	>>> gromacs.config.setup()

GromacsWrapper might need a file ~/.gromacswrapper.cfg with content

[Gromacs]
tools = gmx gmx_d 
# gmx_mpi_d gmx_mpi_d

# name of the logfile that is written to the current directory
logfilename = gromacs.log

# loglevels (see Python's logging module for details)
#   ERROR   only fatal errors
#   WARN    only warnings
#   INFO    interesting messages
#   DEBUG   everything

# console messages written to screen
loglevel_console = INFO

# file messages written to logfilename
loglevel_file = DEBUG

in order to know the GROMACS executables it is allowed to use. Otherwise, calls to gmx_mpi or gmx_mpi_d without MPI wrapper might lead to MPI warnings in output that cause GromacsWrapper to fail.

Logging

In [3]:
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger()
logger.setLevel(logging.INFO)

ParmEd needs to know the GROMACS topology folder, usually get this from envionment variable GMXLIB:

Function definitions

In [4]:
def find_undeclared_variables(infile):
    """identify all variables evaluated in a jinja 2 template file"""
    env = jinja2.Environment()
    with open(infile) as template_file:
        parsed = env.parse(template_file.read())

    undefined = jinja2.meta.find_undeclared_variables(parsed)
    return undefined
In [5]:
def memuse():
    """Quick overview on memory usage of objects in Jupyter notebook"""
    # https://stackoverflow.com/questions/40993626/list-memory-usage-in-ipython-and-jupyter
    # These are the usual ipython objects, including this one you are creating
    ipython_vars = ['In', 'Out', 'exit', 'quit', 'get_ipython', 'ipython_vars']

    # Get a sorted list of the objects and their sizes
    return sorted([(x, sys.getsizeof(globals().get(x))) for x in dir(sys.modules['__main__']) if not x.startswith('_') and x not in sys.modules and x not in ipython_vars], key=lambda x: x[1], reverse=True)

Global settings

In [13]:
# pandas settings
pd.options.display.max_rows = 200
pd.options.display.max_columns = 16
pd.options.display.max_colwidth = 256
In [6]:
os.environ['GMXLIB'] = '/gmx_top'
In [7]:
# pmd.gromacs.GROMACS_TOPDIR = os.environ['GMXLIB']
pmd.gromacs.GROMACS_TOPDIR = '/gmx_top'
In [8]:
# prefix = '/mnt/dat/work/testuser/indenter/sandbox/20191110_packmol'
prefix = '/mnt/dat/work'
In [9]:
work_prefix = '/mnt/dat/work/tmp'
In [10]:
try:
    os.mkdir(work_prefix)
except FileExistsError as exc:
    print(exc)
[Errno 17] File exists: '/mnt/dat/work/tmp'
In [11]:
os.chdir(work_prefix)
In [12]:
# the FireWorks LaunchPad
lp = LaunchPad.auto_load() #Define the server and database
# FilePad behaves analogous to LaunchPad
fp = FilePad.auto_load()

Conversion from LAMMPS data format to PDB

The following bash / tcl snippet converts a LAMMPS data file to PDB, assigning the desired names as mapped in a yaml file

#!/bin/bash
# echo "package require jlhvmd; jlh lmp2pdb indenter.lammps indenter.pdb" | vmd -eofexit
vmd -eofexit << 'EOF'
package require jlhvmd
topo readlammpsdata indenter.lammps
jlh type2name SDS_type2name.yaml
jlh name2res  SDS_name2res.yaml
set sel [atomselect top all]
$sel writepdb indenter.pdb
EOF

pdb_chain.py indenter.pdb > indenter_wo_chainid.pdb
pdb_reres_by_atom_9999.py indenter_wo_chainid.pdb > indenter_reres.pdb

Requires

Overview

Overview on projects in database

In [14]:
query = {'metadata.datetime': {'$gt': '2020'} }
In [15]:
fp.filepad.count_documents(query)
Out[15]:
11975
In [16]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 'project': '$metadata.project' },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # pull 'project' field up in hierarchy
        "$addFields": { 
            "project": "$_id.project",
        },
    },
    {  # drop nested '_id.project'
        "$project": { 
            "_id": False 
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

# sort_aggregation
#aggregation_pipeline = [ match_aggregation, group_aggregation, set_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [c for c in cursor]
res_df = pd.DataFrame(data=res) # pandas Dataframe is just nice for printing in notebook
In [17]:
res_df
Out[17]:
object_count earliest latest project
0 72 2020-10-25 01:48:28.113800 2020-10-25 01:48:28.245721 2020-10-25-sds-on-au-111-substrate-passivation-trial
1 97 2020-10-24 19:55:53.929728 2020-10-25 00:55:09.723289 2020-10-24-sds-on-au-111-substrate-passivation-trial
2 53 2020-10-24 19:50:57.364604 2020-10-24 19:50:57.367249 2020-10-24-au-111-150x150x150-fcc-substrate-creation
3 53 2020-10-20 00:36:42.139788 2020-10-20 00:36:42.145747 2020-10-19-au-111-150x150x150-fcc-substrate-creation
4 2815 2020-10-13 23:31:57.716886 2020-10-13 23:31:58.871696 2020-10-13-ctab-on-au-111-substrate-passivation
5 167 2020-10-11 00:52:32.501863 2020-10-11 21:47:34.277020 2020-10-11-ctab-on-au-111-substrate-passivation-trial
6 9 2020-10-10 19:02:26.582714 2020-10-10 19:02:26.667597 2020-10-10-ctab-on-au-111-substrate-passivation-trial
7 68 2020-10-05 23:58:54.069384 2020-10-05 23:58:54.150170 2020-10-05-ctab-on-au-111-substrate-passivation-trial
8 68 2020-10-03 13:58:43.057925 2020-10-03 13:58:43.176783 2020-10-03-ctab-on-au-111-substrate-passivation-trial
9 3 2020-10-02 20:17:13.935637 2020-10-02 20:17:14.015525 2020-10-02-ctab-on-au-111-substrate-passivation-trial
10 6 2020-10-01 16:38:35.447564 2020-10-01 21:49:44.957275 2020-10-01-ctab-on-au-111-substrate-passivation-trial
11 3 2020-09-30 00:59:24.296631 2020-09-30 00:59:24.381181 2020-09-30-ctab-on-au-111-substrate-passivation-trial
12 2703 2020-09-28 02:11:38.861517 2020-09-28 02:11:42.558642 2020-09-28-ctab-on-au-111-substrate-passivation
13 53 2020-09-27 18:58:47.134481 2020-09-27 18:58:47.137826 2020-09-27-au-111-fcc-substrate-creation
14 132 2020-09-27 18:39:55.970548 2020-09-27 18:39:56.179259 2020-09-27-ctab-on-au-111-substrate-passivation-trial
15 53 2020-09-26 14:45:31.896748 2020-09-26 14:45:31.898524 2020-09-26-au-111-fcc-substrate-creation-trial
16 92 2020-09-26 00:31:02.102804 2020-09-26 00:31:02.270975 2020-09-25-ctab-on-au-111-substrate-passivation
17 80 2020-09-25 19:25:17.206266 2020-09-25 23:20:46.761970 2020-09-25-au-111-fcc-substrate-creation-trial
18 56 2020-09-25 19:07:28.245703 2020-09-26 00:33:42.499737 2020-09-25-au-111-fcc-substrate-creation
19 2844 2020-09-14 19:40:24.649384 2020-09-14 19:40:26.998397 2020-09-14-sds-on-au-111-substrate-passivation
20 421 2020-09-09 23:24:22.512782 2020-09-09 23:24:23.635704 2020-09-10-sds-on-au-111-substrate-passivation-trial
21 210 2020-09-08 23:15:38.029121 2020-09-09 17:35:18.670720 2020-09-09-sds-on-au-111-substrate-passivation-trial
22 252 2020-09-08 18:12:59.181303 2020-09-08 18:12:59.406524 2020-09-08-sds-on-au-111-substrate-passivation-trial
23 343 2020-09-03 15:46:52.139300 2020-09-03 23:22:15.222281 2020-09-03-sds-on-au-111-substrate-passivation-trial
24 245 2020-09-01 16:07:48.182428 2020-09-02 15:39:12.955771 2020-09-01-sds-on-au-111-substrate-passivation-trial
25 52 2020-08-31 02:32:35.171803 2020-09-01 00:35:40.345368 2020-08-31-sds-on-au-111-substrate-passivation-trial
26 3 2020-08-31 01:32:13.820858 2020-08-31 01:32:13.902597 2020-08-30-sds-on-au-111-substrate-passivation-trial
27 6 2020-08-28 00:14:08.820442 2020-08-28 00:35:31.724026 2020-08-27-sds-on-au-111-substrate-passivation-trial
28 80 2020-08-24 17:48:58.997210 2020-08-24 20:24:33.489028 2020-08-24-au-111-fcc-substrate-creation-trial
29 537 2020-07-29 03:50:20.375090 2020-07-29 03:50:22.884335 2020-07-29-ctab-on-au-111-indenter-passivation
30 399 2020-07-29 03:47:40.301419 2020-07-29 03:47:42.358240 2020-07-29-sds-on-au-111-indenter-passivation

Overview on steps in project

In [18]:
project_id = '2020-10-13-ctab-on-au-111-substrate-passivation'
In [19]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
}
In [20]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[20]:
2824
In [21]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['step', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [22]:
res_df
Out[22]:
step earliest latest object_count
0 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad 2020-10-13 23:31:57.836878 2020-10-13 23:31:58.351891 206
1 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad 2020-10-13 23:31:57.830704 2020-10-13 23:31:58.346478 252
2 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad 2020-10-13 23:31:57.825805 2020-10-13 23:31:58.642317 273
3 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad 2020-10-13 23:31:57.819787 2020-10-13 23:31:58.871696 483
4 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad 2020-10-13 23:31:57.815064 2020-10-13 23:31:58.866987 48
5 SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad 2020-10-13 23:31:57.814932 2020-10-13 23:31:58.866857 48
6 SubstratePassivation:CylindricalPackingAndEquilibartion:PDBCleanup:push_filepad 2020-10-13 23:31:57.814621 2020-10-13 23:31:58.866480 24
7 SubstratePassivation:CylindricalPackingAndEquilibartion:CylindricalPacking:CylindricalPackingMain:push_filepad 2020-10-13 23:31:57.814415 2020-10-13 23:31:58.866236 24
8 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad 2020-10-13 23:31:57.814026 2020-10-13 23:31:58.865832 176
9 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad 2020-10-13 23:31:57.808419 2020-10-13 23:31:58.860104 315
10 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad 2020-10-13 23:31:57.803220 2020-10-13 23:31:58.855226 357
11 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad 2020-10-13 23:31:57.798467 2020-10-13 23:31:58.850377 462
12 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad 2020-10-13 23:31:57.793538 2020-10-13 23:31:58.844403 48
13 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad 2020-10-13 23:31:57.793400 2020-10-13 23:31:58.844100 48
14 SubstratePassivation:BilayerPackingAndEquilibartion:PDBCleanup:push_filepad 2020-10-13 23:31:57.793073 2020-10-13 23:31:58.843344 24
15 SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_filepad 2020-10-13 23:31:57.792866 2020-10-13 23:31:58.842868 24
16 SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad 2020-10-13 23:31:57.792495 2020-10-13 23:31:57.792501 2
17 SubstratePassivation:ComponentMeasures:SubstratePreparation:FormatConversion:push_filepad 2020-10-13 23:31:57.716886 2020-10-13 23:31:57.716886 1
18 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsTrajectoryVisualization:push_infiles None None 1
19 SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles None None 2
20 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:GromacsNPTEquilibrationMain:push_infiles None None 1
21 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:GromacsPrepMain:push_infiles None None 1
22 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsEnergyMinimizationAfterSolvationMain:push_infiles None None 1
23 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:GromacsRelaxationMain:push_infiles None None 1
24 SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:SurfactantMoleculeMeasuresMain:push_infiles None None 1
25 SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:GromacsNVTEquilibrationMain:push_infiles None None 1
In [23]:
res_df['step'].values
Out[23]:
array(['SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:PDBCleanup:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:CylindricalPacking:CylindricalPackingMain:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:PDBCleanup:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_filepad',
       'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad',
       'SubstratePassivation:ComponentMeasures:SubstratePreparation:FormatConversion:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsTrajectoryVisualization:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:GromacsNPTEquilibrationMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:GromacsPrepMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsEnergyMinimizationAfterSolvationMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:GromacsRelaxationMain:push_infiles',
       'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:SurfactantMoleculeMeasuresMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:GromacsNVTEquilibrationMain:push_infiles'],
      dtype=object)

Overview on objects in project

In [24]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
}
In [25]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[25]:
2824
In [26]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'step', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [27]:
res_df
Out[27]:
type step name earliest latest object_count
0 mp4_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943535 2020-10-13 23:31:58.157138 4
1 surfactant_tail_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943533 2020-10-13 23:31:58.157136 4
2 surfactant_head_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943531 2020-10-13 23:31:58.157133 4
3 substrate_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943528 2020-10-13 23:31:58.157131 4
4 counterion_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943526 2020-10-13 23:31:58.157128 4
5 surfactant_tail_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943524 2020-10-13 23:31:58.157126 4
6 surfactant_head_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943522 2020-10-13 23:31:58.157124 4
7 surfactant_head_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943520 2020-10-13 23:31:58.157122 4
8 substrate_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943517 2020-10-13 23:31:58.157120 4
9 substrate_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943515 2020-10-13 23:31:58.157117 4
10 counterion_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943513 2020-10-13 23:31:58.157115 4
11 counterion_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943511 2020-10-13 23:31:58.157113 4
12 counterion_substrate_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943508 2020-10-13 23:31:58.157111 4
13 counterion_counterion_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943506 2020-10-13 23:31:58.157108 4
14 index_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943504 2020-10-13 23:31:58.157106 4
15 run_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943502 2020-10-13 23:31:58.157104 4
16 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943499 2020-10-13 23:31:58.157102 4
17 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943497 2020-10-13 23:31:58.157099 4
18 trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943495 2020-10-13 23:31:58.157097 4
19 uncompressed_trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.943492 2020-10-13 23:31:58.157095 4
20 mp4_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921402 2020-10-13 23:31:58.135382 4
21 surfactant_tail_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921399 2020-10-13 23:31:58.135380 4
22 surfactant_head_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921397 2020-10-13 23:31:58.135377 4
23 substrate_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921395 2020-10-13 23:31:58.135375 4
24 counterion_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921392 2020-10-13 23:31:58.135373 4
25 surfactant_tail_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921390 2020-10-13 23:31:58.135371 4
26 surfactant_head_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921388 2020-10-13 23:31:58.135368 4
27 surfactant_head_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921386 2020-10-13 23:31:58.135366 4
28 substrate_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921383 2020-10-13 23:31:58.135364 4
29 substrate_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921381 2020-10-13 23:31:58.135361 4
30 counterion_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921379 2020-10-13 23:31:58.135359 4
31 counterion_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921376 2020-10-13 23:31:58.135357 4
32 counterion_substrate_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921374 2020-10-13 23:31:58.135355 4
33 counterion_counterion_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921372 2020-10-13 23:31:58.135353 4
34 index_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921370 2020-10-13 23:31:58.135350 4
35 run_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921367 2020-10-13 23:31:58.135348 4
36 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921365 2020-10-13 23:31:58.135346 4
37 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921363 2020-10-13 23:31:58.135344 4
38 trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921361 2020-10-13 23:31:58.135342 4
39 uncompressed_trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.921358 2020-10-13 23:31:58.135339 4
40 energy_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.836888 2020-10-13 23:31:58.351891 42
41 log_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.836885 2020-10-13 23:31:58.351888 42
42 checkpoint_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.836878 2020-10-13 23:31:58.351883 42
43 mp4_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830754 2020-10-13 23:31:58.346478 12
44 surfactant_tail_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830752 2020-10-13 23:31:58.346476 12
45 surfactant_head_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830749 2020-10-13 23:31:58.346474 12
46 substrate_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830747 2020-10-13 23:31:58.346472 12
47 counterion_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830745 2020-10-13 23:31:58.346469 12
48 surfactant_tail_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830743 2020-10-13 23:31:58.346467 12
49 surfactant_head_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830740 2020-10-13 23:31:58.346465 12
50 surfactant_head_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830738 2020-10-13 23:31:58.346463 12
51 substrate_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830736 2020-10-13 23:31:58.346461 12
52 substrate_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830734 2020-10-13 23:31:58.346459 12
53 counterion_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830732 2020-10-13 23:31:58.346457 12
54 counterion_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830729 2020-10-13 23:31:58.346454 12
55 counterion_substrate_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830727 2020-10-13 23:31:58.346452 12
56 counterion_counterion_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830725 2020-10-13 23:31:58.346450 12
57 run_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830723 2020-10-13 23:31:58.346448 12
58 index_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830721 2020-10-13 23:31:58.346446 12
59 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830718 2020-10-13 23:31:58.346443 12
60 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830716 2020-10-13 23:31:58.346441 12
61 trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830714 2020-10-13 23:31:58.346439 12
62 energy_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830711 2020-10-13 23:31:58.346436 12
63 log_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.830704 2020-10-13 23:31:58.346430 12
64 mp4_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825856 2020-10-13 23:31:58.642317 13
65 surfactant_tail_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825854 2020-10-13 23:31:58.642311 13
66 surfactant_head_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825852 2020-10-13 23:31:58.642305 13
67 substrate_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825849 2020-10-13 23:31:58.642300 13
68 counterion_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825847 2020-10-13 23:31:58.642294 13
69 surfactant_tail_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825845 2020-10-13 23:31:58.642288 13
70 surfactant_head_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825843 2020-10-13 23:31:58.642282 13
71 surfactant_head_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825840 2020-10-13 23:31:58.642276 13
72 substrate_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825838 2020-10-13 23:31:58.642270 13
73 substrate_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825836 2020-10-13 23:31:58.642264 13
74 counterion_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825833 2020-10-13 23:31:58.642258 13
75 counterion_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825831 2020-10-13 23:31:58.642252 13
76 counterion_substrate_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825829 2020-10-13 23:31:58.642247 13
77 counterion_counterion_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825826 2020-10-13 23:31:58.642241 13
78 run_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825824 2020-10-13 23:31:58.642236 13
79 index_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825822 2020-10-13 23:31:58.642230 13
80 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825819 2020-10-13 23:31:58.642223 13
81 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825817 2020-10-13 23:31:58.642217 13
82 trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825815 2020-10-13 23:31:58.642211 13
83 energy_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825811 2020-10-13 23:31:58.642204 13
84 log_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.825805 2020-10-13 23:31:58.642192 13
85 mp4_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819837 2020-10-13 23:31:58.871696 23
86 surfactant_tail_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819835 2020-10-13 23:31:58.871693 23
87 surfactant_head_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819832 2020-10-13 23:31:58.871691 23
88 substrate_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819830 2020-10-13 23:31:58.871689 23
89 counterion_rmsd SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819828 2020-10-13 23:31:58.871687 23
90 surfactant_tail_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819826 2020-10-13 23:31:58.871685 23
91 surfactant_head_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819823 2020-10-13 23:31:58.871682 23
92 surfactant_head_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819821 2020-10-13 23:31:58.871680 23
93 substrate_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819819 2020-10-13 23:31:58.871678 23
94 substrate_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819817 2020-10-13 23:31:58.871676 23
95 counterion_surfactant_tail_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819814 2020-10-13 23:31:58.871674 23
96 counterion_surfactant_head_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819812 2020-10-13 23:31:58.871671 23
97 counterion_substrate_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819810 2020-10-13 23:31:58.871669 23
98 counterion_counterion_rdf SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819807 2020-10-13 23:31:58.871667 23
99 trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819805 2020-10-13 23:31:58.871665 23
100 run_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819803 2020-10-13 23:31:58.871663 23
101 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819801 2020-10-13 23:31:58.871660 23
102 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819798 2020-10-13 23:31:58.871658 23
103 uncompressed_trajectory_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819796 2020-10-13 23:31:58.871656 23
104 energy_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819793 2020-10-13 23:31:58.871653 23
105 log_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.819787 2020-10-13 23:31:58.871647 23
106 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad NaN 2020-10-13 23:31:57.815068 2020-10-13 23:31:58.866987 24
107 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad NaN 2020-10-13 23:31:57.815064 2020-10-13 23:31:58.866984 24
108 topology_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad NaN 2020-10-13 23:31:57.814935 2020-10-13 23:31:58.866857 24
109 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad NaN 2020-10-13 23:31:57.814932 2020-10-13 23:31:58.866854 24
110 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:PDBCleanup:push_filepad NaN 2020-10-13 23:31:57.814621 2020-10-13 23:31:58.866480 24
111 data_file SubstratePassivation:CylindricalPackingAndEquilibartion:CylindricalPacking:CylindricalPackingMain:push_filepad NaN 2020-10-13 23:31:57.814415 2020-10-13 23:31:58.866236 24
112 energy_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.814034 2020-10-13 23:31:58.865832 32
113 log_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.814031 2020-10-13 23:31:58.865829 32
114 checkpoint_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad NaN 2020-10-13 23:31:57.814026 2020-10-13 23:31:58.865822 32
115 mp4_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808469 2020-10-13 23:31:58.860104 15
116 surfactant_tail_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808467 2020-10-13 23:31:58.860101 15
117 surfactant_head_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808464 2020-10-13 23:31:58.860099 15
118 substrate_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808462 2020-10-13 23:31:58.860097 15
119 counterion_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808460 2020-10-13 23:31:58.860095 15
120 surfactant_tail_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808458 2020-10-13 23:31:58.860092 15
121 surfactant_head_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808455 2020-10-13 23:31:58.860090 15
122 surfactant_head_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808453 2020-10-13 23:31:58.860088 15
123 substrate_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808451 2020-10-13 23:31:58.860086 15
124 substrate_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808449 2020-10-13 23:31:58.860084 15
125 counterion_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808446 2020-10-13 23:31:58.860081 15
126 counterion_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808444 2020-10-13 23:31:58.860079 15
127 counterion_substrate_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808442 2020-10-13 23:31:58.860076 15
128 counterion_counterion_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808440 2020-10-13 23:31:58.860074 15
129 run_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808438 2020-10-13 23:31:58.860072 15
130 index_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808435 2020-10-13 23:31:58.860070 15
131 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808433 2020-10-13 23:31:58.860067 15
132 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808431 2020-10-13 23:31:58.860065 15
133 trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808429 2020-10-13 23:31:58.860063 15
134 energy_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808425 2020-10-13 23:31:58.860060 15
135 log_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad NaN 2020-10-13 23:31:57.808419 2020-10-13 23:31:58.860054 15
136 mp4_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803269 2020-10-13 23:31:58.855226 17
137 surfactant_tail_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803267 2020-10-13 23:31:58.855224 17
138 surfactant_head_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803264 2020-10-13 23:31:58.855222 17
139 substrate_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803262 2020-10-13 23:31:58.855219 17
140 counterion_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803260 2020-10-13 23:31:58.855217 17
141 surfactant_tail_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803258 2020-10-13 23:31:58.855215 17
142 surfactant_head_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803256 2020-10-13 23:31:58.855213 17
143 surfactant_head_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803253 2020-10-13 23:31:58.855211 17
144 substrate_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803251 2020-10-13 23:31:58.855208 17
145 substrate_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803249 2020-10-13 23:31:58.855206 17
146 counterion_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803247 2020-10-13 23:31:58.855204 17
147 counterion_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803244 2020-10-13 23:31:58.855202 17
148 counterion_substrate_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803242 2020-10-13 23:31:58.855199 17
149 counterion_counterion_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803240 2020-10-13 23:31:58.855197 17
150 run_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803238 2020-10-13 23:31:58.855195 17
151 index_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803235 2020-10-13 23:31:58.855193 17
152 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803233 2020-10-13 23:31:58.855190 17
153 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803231 2020-10-13 23:31:58.855188 17
154 trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803228 2020-10-13 23:31:58.855186 17
155 energy_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803226 2020-10-13 23:31:58.855183 17
156 log_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad NaN 2020-10-13 23:31:57.803220 2020-10-13 23:31:58.855177 17
157 mp4_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798517 2020-10-13 23:31:58.850377 21
158 surfactant_tail_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798515 2020-10-13 23:31:58.850375 21
159 surfactant_head_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798513 2020-10-13 23:31:58.850373 21
160 substrate_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798510 2020-10-13 23:31:58.850371 21
161 counterion_rmsd SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798508 2020-10-13 23:31:58.850369 21
162 surfactant_tail_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798506 2020-10-13 23:31:58.850366 21
163 surfactant_head_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798504 2020-10-13 23:31:58.850364 22
164 surfactant_head_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798501 2020-10-13 23:31:58.850362 22
165 substrate_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798499 2020-10-13 23:31:58.850360 22
166 substrate_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798497 2020-10-13 23:31:58.850358 22
167 counterion_surfactant_tail_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798495 2020-10-13 23:31:58.850355 22
168 counterion_surfactant_head_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798492 2020-10-13 23:31:58.850353 22
169 counterion_substrate_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798490 2020-10-13 23:31:58.850351 22
170 counterion_counterion_rdf SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798488 2020-10-13 23:31:58.850349 22
171 trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798486 2020-10-13 23:31:58.850347 22
172 run_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798483 2020-10-13 23:31:58.850344 23
173 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798481 2020-10-13 23:31:58.850342 23
174 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798479 2020-10-13 23:31:58.850340 23
175 uncompressed_trajectory_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798476 2020-10-13 23:31:58.850337 23
176 energy_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798473 2020-10-13 23:31:58.850334 23
177 log_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad NaN 2020-10-13 23:31:57.798467 2020-10-13 23:31:58.850328 23
178 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad NaN 2020-10-13 23:31:57.793541 2020-10-13 23:31:58.844403 24
179 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad NaN 2020-10-13 23:31:57.793538 2020-10-13 23:31:58.844395 24
180 topology_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad NaN 2020-10-13 23:31:57.793403 2020-10-13 23:31:58.844100 24
181 data_file SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad NaN 2020-10-13 23:31:57.793400 2020-10-13 23:31:58.844092 24
182 data_file SubstratePassivation:BilayerPackingAndEquilibartion:PDBCleanup:push_filepad NaN 2020-10-13 23:31:57.793073 2020-10-13 23:31:58.843344 24
183 data_file SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_filepad NaN 2020-10-13 23:31:57.792866 2020-10-13 23:31:58.842868 24
184 png_file SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad NaN 2020-10-13 23:31:57.792501 2020-10-13 23:31:57.792501 1
185 surfactant_file SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad NaN 2020-10-13 23:31:57.792495 2020-10-13 23:31:57.792495 1
186 data_file SubstratePassivation:ComponentMeasures:SubstratePreparation:FormatConversion:push_filepad NaN 2020-10-13 23:31:57.716886 2020-10-13 23:31:57.716886 1
187 surfactant_file SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:SurfactantMoleculeMeasuresMain:push_infiles 1_CTAB.pdb None None 1
188 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:GromacsRelaxationMain:push_infiles relax_z_only.mdp None None 1
189 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:GromacsPrepMain:push_infiles sys.top.template None None 1
190 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsTrajectoryVisualization:push_infiles view.pml.template None None 1
191 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:GromacsNVTEquilibrationMain:push_infiles nvt.mdp None None 1
192 template SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles flat.inp.template None None 1
193 counterion_file SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles 1_BR.pdb None None 1
194 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsEnergyMinimizationAfterSolvationMain:push_infiles em_solvated.mdp None None 1
195 input SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:GromacsNPTEquilibrationMain:push_infiles npt_z_only.mdp None None 1

Overview on images by distinct steps

In [28]:
query = {
    'metadata.project': project_id,
    'metadata.type': 'png_file',
}
In [29]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[29]:
1
In [30]:
# check files degenerate by 'metadata.type' ad 'metadata.name'

aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['step', 'type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [31]:
res_df
Out[31]:
step type name earliest latest object_count
0 SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad png_file NaN 2020-10-13 23:31:57.792501 2020-10-13 23:31:57.792501 1
In [32]:
res_df["step"][0]
Out[32]:
'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad'

Packing visualization

Surfactant measures

In [33]:
query = {
    'metadata.project': project_id,
    'metadata.type': 'png_file',
    'metadata.step': {'$regex': 'SurfactantMoleculeMeasures'}
}
In [34]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[34]:
1
In [35]:
# check files degenerate by 'metadata.type' ad 'metadata.name'

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["gfs_id"])
    with tempfile.NamedTemporaryFile(suffix='.png') as tmp:
        tmp.write(content)
        obj_list.append(Image(filename=tmp.name)) 
    print('.',end='')
.
In [36]:
obj_list[0]
Out[36]:

Energy minimization after solvation analysis

Overview on objects in step

In [37]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'}
}
In [38]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[38]:
947
In [39]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [40]:
res_df
Out[40]:
type name earliest latest object_count
0 mp4_file NaN 2020-10-13 23:31:57.798517 2020-10-13 23:31:58.871696 44
1 surfactant_tail_rmsd NaN 2020-10-13 23:31:57.798515 2020-10-13 23:31:58.871693 44
2 surfactant_head_rmsd NaN 2020-10-13 23:31:57.798513 2020-10-13 23:31:58.871691 44
3 substrate_rmsd NaN 2020-10-13 23:31:57.798510 2020-10-13 23:31:58.871689 44
4 counterion_rmsd NaN 2020-10-13 23:31:57.798508 2020-10-13 23:31:58.871687 44
5 surfactant_tail_surfactant_tail_rdf NaN 2020-10-13 23:31:57.798506 2020-10-13 23:31:58.871685 44
6 surfactant_head_surfactant_tail_rdf NaN 2020-10-13 23:31:57.798504 2020-10-13 23:31:58.871682 45
7 surfactant_head_surfactant_head_rdf NaN 2020-10-13 23:31:57.798501 2020-10-13 23:31:58.871680 45
8 substrate_surfactant_tail_rdf NaN 2020-10-13 23:31:57.798499 2020-10-13 23:31:58.871678 45
9 substrate_surfactant_head_rdf NaN 2020-10-13 23:31:57.798497 2020-10-13 23:31:58.871676 45
10 counterion_surfactant_tail_rdf NaN 2020-10-13 23:31:57.798495 2020-10-13 23:31:58.871674 45
11 counterion_surfactant_head_rdf NaN 2020-10-13 23:31:57.798492 2020-10-13 23:31:58.871671 45
12 counterion_substrate_rdf NaN 2020-10-13 23:31:57.798490 2020-10-13 23:31:58.871669 45
13 counterion_counterion_rdf NaN 2020-10-13 23:31:57.798488 2020-10-13 23:31:58.871667 45
14 trajectory_file NaN 2020-10-13 23:31:57.798486 2020-10-13 23:31:58.871665 45
15 run_file NaN 2020-10-13 23:31:57.798483 2020-10-13 23:31:58.871663 46
16 topology_file NaN 2020-10-13 23:31:57.798481 2020-10-13 23:31:58.871660 46
17 data_file NaN 2020-10-13 23:31:57.798479 2020-10-13 23:31:58.871658 46
18 uncompressed_trajectory_file NaN 2020-10-13 23:31:57.798476 2020-10-13 23:31:58.871656 46
19 energy_file NaN 2020-10-13 23:31:57.798473 2020-10-13 23:31:58.871653 46
20 log_file NaN 2020-10-13 23:31:57.798467 2020-10-13 23:31:58.871647 46
21 input view.pml.template None None 1
22 input em_solvated.mdp None None 1

Global observables

In [41]:
query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'},
    "metadata.type": 'energy_file',
}
fp.filepad.count_documents(query)
Out[41]:
46
In [60]:
#parameter_dict = {'nmolecules': 'metadata.system.surfactant.nmolecules'}
#parameter_dict = {'shape': 'metadata.system.surfactant.aggregates.shape'}
parameter_dict = {
    'nmolecules': 'metadata.system.surfactant.nmolecules',
    'shape': 'metadata.system.surfactant.aggregates.shape'
}
In [61]:
parameter_keys = list(parameter_dict.keys())
In [62]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)
In [66]:
res_mi_list = []

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        try:
            em_df = panedr.edr_to_df(tmp.name)
        except:
            logger.warning("Failed reading edr for {}".format(metadata))
            continue
        
        mi = pd.MultiIndex.from_product(
            [c["_id"].values(),em_df.index],
            names=[*c["_id"].keys(),'step'])
        em_mi_df = em_df.set_index(mi)        
        res_mi_list.append(em_mi_df)
    print('.',end='')
print('')

res_mi_df = pd.concat(res_mi_list)
res_df = res_mi_df.reset_index()
WARNING:root:Failed reading edr for {'_id': ObjectId('5f8673106b7f8f8ab3bb6dd7'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-07-777197/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-07-777197/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.970518', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on Au(111) substrate passivation', 'owners': [{'name': 'Johannes Laurin Hörmann', 'email': 'johannes.hoermann@imtek.uni-freiburg.de', 'username': 'fr_jh1130', 'orcid': '0000-0001-5867-695X'}], 'machine': 'juwels', 'mode': 'production', 'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules', 'm': 'system->counterion->nmolecules', 's': 'system->surfactant->aggregates->shape'}, 'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'}, {'n': 81, 'm': 81, 's': 'cylinders'}, {'n': 162, 'm': 162, 's': 'bilayer'}, {'n': 162, 'm': 162, 's': 'cylinders'}, {'n': 243, 'm': 243, 's': 'bilayer'}, {'n': 243, 'm': 243, 's': 'cylinders'}, {'n': 324, 'm': 324, 's': 'bilayer'}, {'n': 324, 'm': 324, 's': 'cylinders'}, {'n': 405, 'm': 405, 's': 'bilayer'}, {'n': 405, 'm': 405, 's': 'cylinders'}, {'n': 486, 'm': 486, 's': 'bilayer'}, {'n': 486, 'm': 486, 's': 'cylinders'}, {'n': 567, 'm': 567, 's': 'bilayer'}, {'n': 567, 'm': 567, 's': 'cylinders'}, {'n': 648, 'm': 648, 's': 'bilayer'}, {'n': 648, 'm': 648, 's': 'cylinders'}, {'n': 729, 'm': 729, 's': 'bilayer'}, {'n': 729, 'm': 729, 's': 'cylinders'}, {'n': 810, 'm': 810, 's': 'bilayer'}, {'n': 810, 'm': 810, 's': 'cylinders'}, {'n': 891, 'm': 891, 's': 'bilayer'}, {'n': 891, 'm': 891, 's': 'cylinders'}, {'n': 972, 'm': 972, 's': 'bilayer'}, {'n': 972, 'm': 972, 's': 'cylinders'}, {'n': 1053, 'm': 1053, 's': 'bilayer'}, {'n': 1053, 'm': 1053, 's': 'cylinders'}, {'n': 1134, 'm': 1134, 's': 'bilayer'}, {'n': 1134, 'm': 1134, 's': 'cylinders'}, {'n': 1215, 'm': 1215, 's': 'bilayer'}, {'n': 1215, 'm': 1215, 's': 'cylinders'}, {'n': 1296, 'm': 1296, 's': 'bilayer'}, {'n': 1296, 'm': 1296, 's': 'cylinders'}, {'n': 1377, 'm': 1377, 's': 'bilayer'}, {'n': 1377, 'm': 1377, 's': 'cylinders'}, {'n': 1458, 'm': 1458, 's': 'bilayer'}, {'n': 1458, 'm': 1458, 's': 'cylinders'}, {'n': 1539, 'm': 1539, 's': 'bilayer'}, {'n': 1539, 'm': 1539, 's': 'cylinders'}, {'n': 1620, 'm': 1620, 's': 'bilayer'}, {'n': 1620, 'm': 1620, 's': 'cylinders'}, {'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 405, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 405, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'bilayer'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': {'type': 11}, 'measures': [198.82074920012752, 199.633414036829, 197.62699714360895], 'name': 'AUM', 'resname': 'AUM', 'reference_atom': {'name': 'AU'}, 'length': 198.82074920012752, 'width': 199.633414036829, 'height': 197.62699714360895, 'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]], 'natoms': 463680}, 'solvent': {'name': 'H2O', 'resname': 'SOL', 'reference_atom': {'name': 'OW'}, 'height': 180.0}, 'box': {'length': 198.82074920012752, 'width': 199.633414036829, 'height': 377.62699714360895}}, 'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'}, 'element_to_pdb_atom_name_mapping': {'Au': 'AU'}, 'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}}, 'packing': {'surfactant_substrate': {'tolerance': 1.5, 'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617], [100.226, 100.354, 126.03802096329918]], 'lower_constraint_plane': 105.37984599543711, 'upper_constraint_plane': 122.27517496786207}, {'bounding_box': [[-98.572, -99.281, 126.03802096329918], [100.226, 100.354, 150.45904192659833]], 'lower_constraint_plane': 129.80086695873626, 'upper_constraint_plane': 146.69619593116124}]}}}, 'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS', 'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation', 'uuid': '87e45e19-718a-4be4-a0ab-6f51a2ed8c51', 'name': '2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation'}, 'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-34-42-560984/2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation', 'uuid': '87e45e19-718a-4be4-a0ab-6f51a2ed8c51', 'name': '2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-34-42-560984/2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation', 'uuid': '87e45e19-718a-4be4-a0ab-6f51a2ed8c51', 'name': '2020-10-13-23-31-57-968138-n-405-m-405-s-bilayer-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.191202', 'expiration_date': '2022-10-13 23:31:15.191202', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f8673106b7f8f8ab3bb6dd5'}
WARNING:root:Failed reading edr for {'_id': ObjectId('5f8676848752d7b81fa6db67'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-50-56-222897/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-50-56-222897/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.819837', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on Au(111) substrate passivation', 'owners': [{'name': 'Johannes Laurin Hörmann', 'email': 'johannes.hoermann@imtek.uni-freiburg.de', 'username': 'fr_jh1130', 'orcid': '0000-0001-5867-695X'}], 'machine': 'juwels', 'mode': 'production', 'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules', 'm': 'system->counterion->nmolecules', 's': 'system->surfactant->aggregates->shape'}, 'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'}, {'n': 81, 'm': 81, 's': 'cylinders'}, {'n': 162, 'm': 162, 's': 'bilayer'}, {'n': 162, 'm': 162, 's': 'cylinders'}, {'n': 243, 'm': 243, 's': 'bilayer'}, {'n': 243, 'm': 243, 's': 'cylinders'}, {'n': 324, 'm': 324, 's': 'bilayer'}, {'n': 324, 'm': 324, 's': 'cylinders'}, {'n': 405, 'm': 405, 's': 'bilayer'}, {'n': 405, 'm': 405, 's': 'cylinders'}, {'n': 486, 'm': 486, 's': 'bilayer'}, {'n': 486, 'm': 486, 's': 'cylinders'}, {'n': 567, 'm': 567, 's': 'bilayer'}, {'n': 567, 'm': 567, 's': 'cylinders'}, {'n': 648, 'm': 648, 's': 'bilayer'}, {'n': 648, 'm': 648, 's': 'cylinders'}, {'n': 729, 'm': 729, 's': 'bilayer'}, {'n': 729, 'm': 729, 's': 'cylinders'}, {'n': 810, 'm': 810, 's': 'bilayer'}, {'n': 810, 'm': 810, 's': 'cylinders'}, {'n': 891, 'm': 891, 's': 'bilayer'}, {'n': 891, 'm': 891, 's': 'cylinders'}, {'n': 972, 'm': 972, 's': 'bilayer'}, {'n': 972, 'm': 972, 's': 'cylinders'}, {'n': 1053, 'm': 1053, 's': 'bilayer'}, {'n': 1053, 'm': 1053, 's': 'cylinders'}, {'n': 1134, 'm': 1134, 's': 'bilayer'}, {'n': 1134, 'm': 1134, 's': 'cylinders'}, {'n': 1215, 'm': 1215, 's': 'bilayer'}, {'n': 1215, 'm': 1215, 's': 'cylinders'}, {'n': 1296, 'm': 1296, 's': 'bilayer'}, {'n': 1296, 'm': 1296, 's': 'cylinders'}, {'n': 1377, 'm': 1377, 's': 'bilayer'}, {'n': 1377, 'm': 1377, 's': 'cylinders'}, {'n': 1458, 'm': 1458, 's': 'bilayer'}, {'n': 1458, 'm': 1458, 's': 'cylinders'}, {'n': 1539, 'm': 1539, 's': 'bilayer'}, {'n': 1539, 'm': 1539, 's': 'cylinders'}, {'n': 1620, 'm': 1620, 's': 'bilayer'}, {'n': 1620, 'm': 1620, 's': 'cylinders'}, {'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 81, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 81, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'cylinders'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': {'type': 11}, 'measures': [198.82074920012752, 199.633414036829, 197.62699714360895], 'name': 'AUM', 'resname': 'AUM', 'reference_atom': {'name': 'AU'}, 'length': 198.82074920012752, 'width': 199.633414036829, 'height': 197.62699714360895, 'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]], 'natoms': 463680}, 'solvent': {'name': 'H2O', 'resname': 'SOL', 'reference_atom': {'name': 'OW'}, 'height': 180.0}, 'box': {'length': 198.82074920012752, 'width': 199.633414036829, 'height': 377.62699714360895}}, 'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'}, 'element_to_pdb_atom_name_mapping': {'Au': 'AU'}, 'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}}, 'packing': {'surfactant_substrate': {'tolerance': 1.5, 'constraints': {'cylinders': [{'base_center': [-98.572, -66.00850000000001, 132.03802096329918], 'r_inner': 1.5, 'r_inner_constraint': 9.025691990874208, 'r_outer_constraint': 22.895328972424956, 'r_outer': 30.421020963299163, 'length': 198.798}, {'base_center': [-98.572, 0.5364999999999895, 132.03802096329918], 'r_inner': 1.5, 'r_inner_constraint': 9.025691990874208, 'r_outer_constraint': 22.895328972424956, 'r_outer': 30.421020963299163, 'length': 198.798}, {'base_center': [-98.572, 67.0815, 132.03802096329918], 'r_inner': 1.5, 'r_inner_constraint': 9.025691990874208, 'r_outer_constraint': 22.895328972424956, 'r_outer': 30.421020963299163, 'length': 198.798}], 'N': 3}}}, 'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS', 'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation', 'uuid': '087aa895-bf32-4c61-bf79-246813c2fde5', 'name': '2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation'}, 'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-47-51-715849/2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation', 'uuid': '087aa895-bf32-4c61-bf79-246813c2fde5', 'name': '2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-47-51-715849/2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation', 'uuid': '087aa895-bf32-4c61-bf79-246813c2fde5', 'name': '2020-10-13-23-31-57-817483-n-81-m-81-s-cylinders-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.182978', 'expiration_date': '2022-10-13 23:31:15.182978', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f8676848752d7b81fa6db65'}
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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8673158752d7b81fa6a964'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-15-857135/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-15-857135/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.949348', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8676eafd2a730dccbb5701'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-52-55-382749/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-52-55-382749/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.798517', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8692ae0bda12f287bbcff2'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-50-40-978193/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-50-40-978193/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.332801', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-50-15-889325/2020-10-13-23-31-58-330427-n-1053-m-1053-s-cylinders-substratepassivation', 'uuid': 'e2de345d-edce-4f8c-9677-fea00bf9d617', 'name': '2020-10-13-23-31-58-330427-n-1053-m-1053-s-cylinders-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-50-15-889325/2020-10-13-23-31-58-330427-n-1053-m-1053-s-cylinders-substratepassivation', 'uuid': 'e2de345d-edce-4f8c-9677-fea00bf9d617', 'name': '2020-10-13-23-31-58-330427-n-1053-m-1053-s-cylinders-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.209046', 'expiration_date': '2022-10-13 23:31:15.209046', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f8692ae0bda12f287bbcff0'}
WARNING:root:Failed reading edr for {'_id': ObjectId('5f867458fd2a730dccbb400b'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-35-421040/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-35-421040/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.906330', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8692fffd2a730dccbbbf88'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-52-18-373474/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-52-18-373474/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.291287', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8675eb6b7f8f8ab3bbb881'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-48-11-416867/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-48-11-416867/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.843254', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f867bd2fd2a730dccbb7218'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-13-07-785424/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-13-07-785424/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.119601', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f868d360bda12f287bb93c8'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-27-23-401884/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-27-23-401884/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.163404', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f86de7a8752d7b81fa7d581'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-11-12-56-357222/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-11-12-56-357222/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.850377', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f86a34efd2a730dccbbdafd'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-25-418263/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-25-418263/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.736016', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f866feb6b7f8f8ab3bb20d8'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-22-45-429402/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-22-45-429402/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.992373', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f86919a0bda12f287bbb580'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-49-57-414265/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-49-57-414265/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.466124', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f86dd716b7f8f8ab3bbf885'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-11-13-32-031541/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-11-13-32-031541/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.871696', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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'm': 648, 's': 'cylinders'}, {'n': 729, 'm': 729, 's': 'bilayer'}, {'n': 729, 'm': 729, 's': 'cylinders'}, {'n': 810, 'm': 810, 's': 'bilayer'}, {'n': 810, 'm': 810, 's': 'cylinders'}, {'n': 891, 'm': 891, 's': 'bilayer'}, {'n': 891, 'm': 891, 's': 'cylinders'}, {'n': 972, 'm': 972, 's': 'bilayer'}, {'n': 972, 'm': 972, 's': 'cylinders'}, {'n': 1053, 'm': 1053, 's': 'bilayer'}, {'n': 1053, 'm': 1053, 's': 'cylinders'}, {'n': 1134, 'm': 1134, 's': 'bilayer'}, {'n': 1134, 'm': 1134, 's': 'cylinders'}, {'n': 1215, 'm': 1215, 's': 'bilayer'}, {'n': 1215, 'm': 1215, 's': 'cylinders'}, {'n': 1296, 'm': 1296, 's': 'bilayer'}, {'n': 1296, 'm': 1296, 's': 'cylinders'}, {'n': 1377, 'm': 1377, 's': 'bilayer'}, {'n': 1377, 'm': 1377, 's': 'cylinders'}, {'n': 1458, 'm': 1458, 's': 'bilayer'}, {'n': 1458, 'm': 1458, 's': 'cylinders'}, {'n': 1539, 'm': 1539, 's': 'bilayer'}, {'n': 1539, 'm': 1539, 's': 'cylinders'}, {'n': 1620, 'm': 1620, 's': 'bilayer'}, {'n': 1620, 'm': 1620, 's': 'cylinders'}, {'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 1377, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 1377, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'bilayer'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': {'type': 11}, 'measures': [198.82074920012752, 199.633414036829, 197.62699714360895], 'name': 'AUM', 'resname': 'AUM', 'reference_atom': {'name': 'AU'}, 'length': 198.82074920012752, 'width': 199.633414036829, 'height': 197.62699714360895, 'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]], 'natoms': 463680}, 'solvent': {'name': 'H2O', 'resname': 'SOL', 'reference_atom': {'name': 'OW'}, 'height': 180.0}, 'box': {'length': 198.82074920012752, 'width': 199.633414036829, 'height': 377.62699714360895}}, 'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'}, 'element_to_pdb_atom_name_mapping': {'Au': 'AU'}, 'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}}, 'packing': {'surfactant_substrate': {'tolerance': 1.5, 'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617], [100.226, 100.354, 126.03802096329918]], 'lower_constraint_plane': 105.37984599543711, 'upper_constraint_plane': 122.27517496786207}, {'bounding_box': [[-98.572, -99.281, 126.03802096329918], [100.226, 100.354, 150.45904192659833]], 'lower_constraint_plane': 129.80086695873626, 'upper_constraint_plane': 146.69619593116124}]}}}, 'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS', 'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation', 'uuid': '4f2b47ce-35e0-44ee-afd9-2af171a2c5f1', 'name': '2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation'}, 'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-25-16-03-28-746638/2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation', 'uuid': '4f2b47ce-35e0-44ee-afd9-2af171a2c5f1', 'name': '2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-25-16-03-28-746638/2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation', 'uuid': '4f2b47ce-35e0-44ee-afd9-2af171a2c5f1', 'name': '2020-10-13-23-31-58-484276-n-1377-m-1377-s-bilayer-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.216044', 'expiration_date': '2022-10-13 23:31:15.216044', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f95a4ad7d270025bd0c8184'}
WARNING:root:Failed reading edr for {'_id': ObjectId('5f8f1416dd26cd5935f45ebe'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-37-19-521230/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-37-19-521230/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.444974', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on Au(111) substrate passivation', 'owners': [{'name': 'Johannes Laurin Hörmann', 'email': 'johannes.hoermann@imtek.uni-freiburg.de', 'username': 'fr_jh1130', 'orcid': '0000-0001-5867-695X'}], 'machine': 'juwels', 'mode': 'production', 'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules', 'm': 'system->counterion->nmolecules', 's': 'system->surfactant->aggregates->shape'}, 'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'}, {'n': 81, 'm': 81, 's': 'cylinders'}, {'n': 162, 'm': 162, 's': 'bilayer'}, {'n': 162, 'm': 162, 's': 'cylinders'}, {'n': 243, 'm': 243, 's': 'bilayer'}, {'n': 243, 'm': 243, 's': 'cylinders'}, {'n': 324, 'm': 324, 's': 'bilayer'}, {'n': 324, 'm': 324, 's': 'cylinders'}, {'n': 405, 'm': 405, 's': 'bilayer'}, {'n': 405, 'm': 405, 's': 'cylinders'}, {'n': 486, 'm': 486, 's': 'bilayer'}, {'n': 486, 'm': 486, 's': 'cylinders'}, {'n': 567, 'm': 567, 's': 'bilayer'}, {'n': 567, 'm': 567, 's': 'cylinders'}, {'n': 648, 'm': 648, 's': 'bilayer'}, {'n': 648, 'm': 648, 's': 'cylinders'}, {'n': 729, 'm': 729, 's': 'bilayer'}, {'n': 729, 'm': 729, 's': 'cylinders'}, {'n': 810, 'm': 810, 's': 'bilayer'}, {'n': 810, 'm': 810, 's': 'cylinders'}, {'n': 891, 'm': 891, 's': 'bilayer'}, {'n': 891, 'm': 891, 's': 'cylinders'}, {'n': 972, 'm': 972, 's': 'bilayer'}, {'n': 972, 'm': 972, 's': 'cylinders'}, {'n': 1053, 'm': 1053, 's': 'bilayer'}, {'n': 1053, 'm': 1053, 's': 'cylinders'}, {'n': 1134, 'm': 1134, 's': 'bilayer'}, {'n': 1134, 'm': 1134, 's': 'cylinders'}, {'n': 1215, 'm': 1215, 's': 'bilayer'}, {'n': 1215, 'm': 1215, 's': 'cylinders'}, {'n': 1296, 'm': 1296, 's': 'bilayer'}, {'n': 1296, 'm': 1296, 's': 'cylinders'}, {'n': 1377, 'm': 1377, 's': 'bilayer'}, {'n': 1377, 'm': 1377, 's': 'cylinders'}, {'n': 1458, 'm': 1458, 's': 'bilayer'}, {'n': 1458, 'm': 1458, 's': 'cylinders'}, {'n': 1539, 'm': 1539, 's': 'bilayer'}, {'n': 1539, 'm': 1539, 's': 'cylinders'}, {'n': 1620, 'm': 1620, 's': 'bilayer'}, {'n': 1620, 'm': 1620, 's': 'cylinders'}, {'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 1296, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 1296, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'bilayer'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': {'type': 11}, 'measures': [198.82074920012752, 199.633414036829, 197.62699714360895], 'name': 'AUM', 'resname': 'AUM', 'reference_atom': {'name': 'AU'}, 'length': 198.82074920012752, 'width': 199.633414036829, 'height': 197.62699714360895, 'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]], 'natoms': 463680}, 'solvent': {'name': 'H2O', 'resname': 'SOL', 'reference_atom': {'name': 'OW'}, 'height': 180.0}, 'box': {'length': 198.82074920012752, 'width': 199.633414036829, 'height': 377.62699714360895}}, 'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'}, 'element_to_pdb_atom_name_mapping': {'Au': 'AU'}, 'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}}, 'packing': {'surfactant_substrate': {'tolerance': 1.5, 'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617], [100.226, 100.354, 126.03802096329918]], 'lower_constraint_plane': 105.37984599543711, 'upper_constraint_plane': 122.27517496786207}, {'bounding_box': [[-98.572, -99.281, 126.03802096329918], [100.226, 100.354, 150.45904192659833]], 'lower_constraint_plane': 129.80086695873626, 'upper_constraint_plane': 146.69619593116124}]}}}, 'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS', 'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}, 'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-29-44-333521/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-29-44-333521/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.214088', 'expiration_date': '2022-10-13 23:31:15.214088', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f8f1416dd26cd5935f45ebc'}

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-66-44729cd44db4> in <module>
     39 print('')
     40 
---> 41 res_mi_df = pd.concat(res_mi_list)
     42 res_df = res_mi_df.reset_index()

/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
    269     ValueError: Indexes have overlapping values: ['a']
    270     """
--> 271     op = _Concatenator(
    272         objs,
    273         axis=axis,

/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py in __init__(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)
    327 
    328         if len(objs) == 0:
--> 329             raise ValueError("No objects to concatenate")
    330 
    331         if keys is None:

ValueError: No objects to concatenate
In [ ]:
res_mi_df
In [64]:
y_quantities = [
    'Potential',
    'Pressure',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

positions = [
    (0,0),
    (0,1),
    (1,0),
    (2,0),
    (2,1),
]
fig, ax = plt.subplots(3,2,figsize=(10,12))
for key, grp in res_df.groupby(parameter_keys[0]):
    for y_quantity, position in zip(y_quantities, positions):
        grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        
fig.tight_layout()

Visualize trajectory

In [67]:
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'},
    'metadata.type': 'mp4_file',
}
In [68]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[68]:
44
In [69]:
# check

aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'nmolecules': '$metadata.system.surfactant.nmolecules'
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

# for i, c in enumerate(cursor): 
#    content, metadata = fp.get_file_by_id(c["latest"])
#    nmolecules = int(c["_id"]["nmolecules"])
    

res = [ {**c['_id'], **c} for c in cursor]
columns = ['nmolecules', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [70]:
res_df
Out[70]:
nmolecules name earliest latest object_count
0 1944 NaN 2020-10-13 23:31:58.850377 2020-10-13 23:31:58.871696 2
1 1863 NaN 2020-10-13 23:31:58.806421 2020-10-13 23:31:58.827543 2
2 1782 NaN 2020-10-13 23:31:58.785597 2020-10-13 23:31:58.785597 1
3 1701 NaN 2020-10-13 23:31:58.659185 2020-10-13 23:31:58.736016 2
4 1620 NaN 2020-10-13 23:31:58.636198 2020-10-13 23:31:58.636198 1
5 1539 NaN 2020-10-13 23:31:58.594170 2020-10-13 23:31:58.594170 1
6 1458 NaN 2020-10-13 23:31:58.529462 2020-10-13 23:31:58.529462 1
7 1377 NaN 2020-10-13 23:31:58.486650 2020-10-13 23:31:58.507798 2
8 1296 NaN 2020-10-13 23:31:58.444974 2020-10-13 23:31:58.466124 2
9 1215 NaN 2020-10-13 23:31:58.400662 2020-10-13 23:31:58.421435 2
10 1134 NaN 2020-10-13 23:31:58.357968 2020-10-13 23:31:58.378932 2
11 1053 NaN 2020-10-13 23:31:58.312030 2020-10-13 23:31:58.332801 2
12 972 NaN 2020-10-13 23:31:58.270321 2020-10-13 23:31:58.291287 2
13 891 NaN 2020-10-13 23:31:58.226158 2020-10-13 23:31:58.248728 2
14 810 NaN 2020-10-13 23:31:58.184143 2020-10-13 23:31:58.205036 2
15 729 NaN 2020-10-13 23:31:58.141455 2020-10-13 23:31:58.163404 2
16 648 NaN 2020-10-13 23:31:58.098172 2020-10-13 23:31:58.119601 2
17 567 NaN 2020-10-13 23:31:58.056085 2020-10-13 23:31:58.076899 2
18 486 NaN 2020-10-13 23:31:58.013506 2020-10-13 23:31:58.035070 2
19 405 NaN 2020-10-13 23:31:57.970518 2020-10-13 23:31:57.992373 2
20 324 NaN 2020-10-13 23:31:57.927512 2020-10-13 23:31:57.949348 2
21 243 NaN 2020-10-13 23:31:57.885000 2020-10-13 23:31:57.906330 2
22 162 NaN 2020-10-13 23:31:57.843254 2020-10-13 23:31:57.864389 2
23 81 NaN 2020-10-13 23:31:57.798517 2020-10-13 23:31:57.819837 2
In [71]:
parameter_keys
Out[71]:
['nmolecules', 'shape']
In [72]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        obj_dict.update({c["_id"][parameter_keys[0]]: Video.from_file(tmp.name)})
    print('.',end='')
............................................
In [73]:
c
Out[73]:
{'_id': {'nmolecules': 81, 'shape': 'bilayer'},
 'degeneracy': 1,
 'latest': '5f8676eafd2a730dccbb56ff'}
In [74]:
for key, obj in obj_dict.items():
    print(key)
    display(obj)
1944
1863
1782
1701
1620
1539
1458
1377
1296
1215
1134
1053
972
891
810
729
648
567
486
405
324
243
162
81

NVT equilibration analysis

Overview on objects in step

In [75]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'}
}
In [76]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[76]:
631
In [77]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [78]:
res_df
Out[78]:
type name earliest latest object_count
0 mp4_file NaN 2020-10-13 23:31:57.803269 2020-10-13 23:31:58.855226 30
1 surfactant_tail_rmsd NaN 2020-10-13 23:31:57.803267 2020-10-13 23:31:58.855224 30
2 surfactant_head_rmsd NaN 2020-10-13 23:31:57.803264 2020-10-13 23:31:58.855222 30
3 substrate_rmsd NaN 2020-10-13 23:31:57.803262 2020-10-13 23:31:58.855219 30
4 counterion_rmsd NaN 2020-10-13 23:31:57.803260 2020-10-13 23:31:58.855217 30
5 surfactant_tail_surfactant_tail_rdf NaN 2020-10-13 23:31:57.803258 2020-10-13 23:31:58.855215 30
6 surfactant_head_surfactant_tail_rdf NaN 2020-10-13 23:31:57.803256 2020-10-13 23:31:58.855213 30
7 surfactant_head_surfactant_head_rdf NaN 2020-10-13 23:31:57.803253 2020-10-13 23:31:58.855211 30
8 substrate_surfactant_tail_rdf NaN 2020-10-13 23:31:57.803251 2020-10-13 23:31:58.855208 30
9 substrate_surfactant_head_rdf NaN 2020-10-13 23:31:57.803249 2020-10-13 23:31:58.855206 30
10 counterion_surfactant_tail_rdf NaN 2020-10-13 23:31:57.803247 2020-10-13 23:31:58.855204 30
11 counterion_surfactant_head_rdf NaN 2020-10-13 23:31:57.803244 2020-10-13 23:31:58.855202 30
12 counterion_substrate_rdf NaN 2020-10-13 23:31:57.803242 2020-10-13 23:31:58.855199 30
13 counterion_counterion_rdf NaN 2020-10-13 23:31:57.803240 2020-10-13 23:31:58.855197 30
14 run_file NaN 2020-10-13 23:31:57.803238 2020-10-13 23:31:58.855195 30
15 index_file NaN 2020-10-13 23:31:57.803235 2020-10-13 23:31:58.855193 30
16 topology_file NaN 2020-10-13 23:31:57.803233 2020-10-13 23:31:58.855190 30
17 data_file NaN 2020-10-13 23:31:57.803231 2020-10-13 23:31:58.855188 30
18 trajectory_file NaN 2020-10-13 23:31:57.803228 2020-10-13 23:31:58.855186 30
19 energy_file NaN 2020-10-13 23:31:57.803226 2020-10-13 23:31:58.855183 30
20 log_file NaN 2020-10-13 23:31:57.803220 2020-10-13 23:31:58.855177 30
21 input nvt.mdp None None 1

Global observables

In [88]:
query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)
Out[88]:
30
In [89]:
parameter_dict = {
    'nmolecules': 'metadata.system.surfactant.nmolecules',
    'shape': 'metadata.system.surfactant.aggregates.shape'
}

parameter_keys = list(parameter_dict.keys())
In [99]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)
In [112]:
res_list = []

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [ *[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()
..............................
In [113]:
res_df.columns
Out[113]:
Index(['nmolecules', 'shape', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')
In [114]:
res_df_mi
Out[114]:
Time Bond U-B Proper Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) ... Coul-SR:rest-rest LJ-SR:rest-rest Coul-14:rest-rest LJ-14:rest-rest T-non-Substrate T-Substrate Lamb-non-Substrate Lamb-Substrate
nmolecules shape step
405 bilayer 0.0 0.0 336.762299 5609.709473 15275.146484 -938.929871 -4.498196e+05 -79815064.0 -12370052.0 ... -12550173.0 1.441314e+06 0.0 0.0 299.153046 0.0 1.0 1.0
1.0 1.0 5569.974609 40000.382812 20775.585938 -77.371773 -4.500497e+05 -80003904.0 -10990010.0 ... -11167832.0 1.273080e+06 0.0 0.0 205.595612 0.0 1.0 1.0
2.0 2.0 6615.566406 46112.875000 21897.025391 148.110474 -4.500002e+05 -80063808.0 -10682512.0 ... -10852491.0 1.223366e+06 0.0 0.0 237.888718 0.0 1.0 1.0
3.0 3.0 7130.301758 50295.371094 22627.021484 302.290680 -4.501067e+05 -80122520.0 -10447955.0 ... -10619445.0 1.171972e+06 0.0 0.0 256.536438 0.0 1.0 1.0
4.0 4.0 7601.223633 53907.386719 22971.468750 399.675079 -4.504439e+05 -80170184.0 -10269777.0 ... -10443889.0 1.129002e+06 0.0 0.0 267.331085 0.0 1.0 1.0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
1296 bilayer 96.0 96.0 26367.396484 191188.453125 78572.117188 2578.112793 -1.441748e+06 -80406624.0 -8529983.0 ... -9151689.0 9.921227e+05 0.0 0.0 298.348053 0.0 1.0 1.0
97.0 97.0 25973.251953 191302.937500 78590.515625 2640.567139 -1.441809e+06 -80405984.0 -8527396.0 ... -9147254.0 9.903748e+05 0.0 0.0 297.865540 0.0 1.0 1.0
98.0 98.0 26293.732422 190148.890625 78993.523438 2589.545166 -1.441626e+06 -80409384.0 -8529375.0 ... -9149565.0 9.883881e+05 0.0 0.0 298.765686 0.0 1.0 1.0
99.0 99.0 26275.277344 190356.203125 78729.914062 2658.798096 -1.441912e+06 -80411120.0 -8522873.0 ... -9144062.0 9.875896e+05 0.0 0.0 298.079498 0.0 1.0 1.0
100.0 100.0 26459.773438 191251.671875 78547.992188 2645.103271 -1.441487e+06 -80403800.0 -8533594.0 ... -9154591.0 9.926151e+05 0.0 0.0 298.365936 0.0 1.0 1.0

3030 rows × 80 columns

In [117]:
#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        
fig.tight_layout()
<ipython-input-117-bb605528b000>:24: UserWarning: Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations
  fig.tight_layout()

Visualize trajectory

In [118]:
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'},
    'metadata.type': 'mp4_file',
}
In [119]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[119]:
30
In [120]:
#parameter_dict = {'nmolecules': 'metadata.system.surfactant.nmolecules'}
#parameter_dict = {'shape': 'metadata.system.surfactant.aggregates.shape'}
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')
..............................
In [121]:
for key, obj in obj_dict.items():
    print(key)
    display(obj)
('cylinders', 1053)
('cylinders', 324)
('cylinders', 162)
('cylinders', 405)
('cylinders', 243)
('cylinders', 567)
('cylinders', 648)
('cylinders', 486)
('cylinders', 81)
('cylinders', 729)
('cylinders', 972)
('cylinders', 1620)
('cylinders', 810)
('bilayer', 729)
('bilayer', 1134)
('bilayer', 81)
('bilayer', 162)
('bilayer', 1053)
('bilayer', 891)
('bilayer', 810)
('bilayer', 1701)
('bilayer', 243)
('bilayer', 486)
('bilayer', 324)
('bilayer', 405)
('bilayer', 1296)
('bilayer', 567)
('bilayer', 648)
('bilayer', 1944)
('bilayer', 972)

NPT equilibration analysis

Overview on objects in step

In [122]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration:push_filepad'}
}
In [123]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[123]:
567
In [124]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [125]:
res_df
Out[125]:
type name earliest latest object_count
0 mp4_file NaN 2020-10-13 23:31:57.808469 2020-10-13 23:31:58.860104 27
1 surfactant_tail_rmsd NaN 2020-10-13 23:31:57.808467 2020-10-13 23:31:58.860101 27
2 surfactant_head_rmsd NaN 2020-10-13 23:31:57.808464 2020-10-13 23:31:58.860099 27
3 substrate_rmsd NaN 2020-10-13 23:31:57.808462 2020-10-13 23:31:58.860097 27
4 counterion_rmsd NaN 2020-10-13 23:31:57.808460 2020-10-13 23:31:58.860095 27
5 surfactant_tail_surfactant_tail_rdf NaN 2020-10-13 23:31:57.808458 2020-10-13 23:31:58.860092 27
6 surfactant_head_surfactant_tail_rdf NaN 2020-10-13 23:31:57.808455 2020-10-13 23:31:58.860090 27
7 surfactant_head_surfactant_head_rdf NaN 2020-10-13 23:31:57.808453 2020-10-13 23:31:58.860088 27
8 substrate_surfactant_tail_rdf NaN 2020-10-13 23:31:57.808451 2020-10-13 23:31:58.860086 27
9 substrate_surfactant_head_rdf NaN 2020-10-13 23:31:57.808449 2020-10-13 23:31:58.860084 27
10 counterion_surfactant_tail_rdf NaN 2020-10-13 23:31:57.808446 2020-10-13 23:31:58.860081 27
11 counterion_surfactant_head_rdf NaN 2020-10-13 23:31:57.808444 2020-10-13 23:31:58.860079 27
12 counterion_substrate_rdf NaN 2020-10-13 23:31:57.808442 2020-10-13 23:31:58.860076 27
13 counterion_counterion_rdf NaN 2020-10-13 23:31:57.808440 2020-10-13 23:31:58.860074 27
14 run_file NaN 2020-10-13 23:31:57.808438 2020-10-13 23:31:58.860072 27
15 index_file NaN 2020-10-13 23:31:57.808435 2020-10-13 23:31:58.860070 27
16 topology_file NaN 2020-10-13 23:31:57.808433 2020-10-13 23:31:58.860067 27
17 data_file NaN 2020-10-13 23:31:57.808431 2020-10-13 23:31:58.860065 27
18 trajectory_file NaN 2020-10-13 23:31:57.808429 2020-10-13 23:31:58.860063 27
19 energy_file NaN 2020-10-13 23:31:57.808425 2020-10-13 23:31:58.860060 27
20 log_file NaN 2020-10-13 23:31:57.808419 2020-10-13 23:31:58.860054 27

Global observables

In [126]:
query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)
Out[126]:
27
In [127]:
metadata = fp.filepad.find_one(query)
In [128]:
metadata
Out[128]:
{'_id': ObjectId('5f8687378752d7b81fa747ec'),
 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-57-308899/default.edr',
 'original_file_name': 'default.edr',
 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-57-308899/default.edr',
 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation',
  'datetime': '2020-10-13 23:31:58.151029',
  'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
  'source_project_id': '2020-09-27-au-111-fcc-substrate-creation',
  'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad',
  'metadata_fp_source_key': 'metadata->system->substrate',
  'metadata_fw_dest_key': 'metadata->system->substrate',
  'metadata_fw_source_key': 'metadata->system->substrate',
  'description': 'CTAB on Au(111) substrate passivation',
  'owners': [{'name': 'Johannes Laurin Hörmann',
    'email': 'johannes.hoermann@imtek.uni-freiburg.de',
    'username': 'fr_jh1130',
    'orcid': '0000-0001-5867-695X'}],
  'machine': 'juwels',
  'mode': 'production',
  'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules',
   'm': 'system->counterion->nmolecules',
   's': 'system->surfactant->aggregates->shape'},
  'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'},
   {'n': 81, 'm': 81, 's': 'cylinders'},
   {'n': 162, 'm': 162, 's': 'bilayer'},
   {'n': 162, 'm': 162, 's': 'cylinders'},
   {'n': 243, 'm': 243, 's': 'bilayer'},
   {'n': 243, 'm': 243, 's': 'cylinders'},
   {'n': 324, 'm': 324, 's': 'bilayer'},
   {'n': 324, 'm': 324, 's': 'cylinders'},
   {'n': 405, 'm': 405, 's': 'bilayer'},
   {'n': 405, 'm': 405, 's': 'cylinders'},
   {'n': 486, 'm': 486, 's': 'bilayer'},
   {'n': 486, 'm': 486, 's': 'cylinders'},
   {'n': 567, 'm': 567, 's': 'bilayer'},
   {'n': 567, 'm': 567, 's': 'cylinders'},
   {'n': 648, 'm': 648, 's': 'bilayer'},
   {'n': 648, 'm': 648, 's': 'cylinders'},
   {'n': 729, 'm': 729, 's': 'bilayer'},
   {'n': 729, 'm': 729, 's': 'cylinders'},
   {'n': 810, 'm': 810, 's': 'bilayer'},
   {'n': 810, 'm': 810, 's': 'cylinders'},
   {'n': 891, 'm': 891, 's': 'bilayer'},
   {'n': 891, 'm': 891, 's': 'cylinders'},
   {'n': 972, 'm': 972, 's': 'bilayer'},
   {'n': 972, 'm': 972, 's': 'cylinders'},
   {'n': 1053, 'm': 1053, 's': 'bilayer'},
   {'n': 1053, 'm': 1053, 's': 'cylinders'},
   {'n': 1134, 'm': 1134, 's': 'bilayer'},
   {'n': 1134, 'm': 1134, 's': 'cylinders'},
   {'n': 1215, 'm': 1215, 's': 'bilayer'},
   {'n': 1215, 'm': 1215, 's': 'cylinders'},
   {'n': 1296, 'm': 1296, 's': 'bilayer'},
   {'n': 1296, 'm': 1296, 's': 'cylinders'},
   {'n': 1377, 'm': 1377, 's': 'bilayer'},
   {'n': 1377, 'm': 1377, 's': 'cylinders'},
   {'n': 1458, 'm': 1458, 's': 'bilayer'},
   {'n': 1458, 'm': 1458, 's': 'cylinders'},
   {'n': 1539, 'm': 1539, 's': 'bilayer'},
   {'n': 1539, 'm': 1539, 's': 'cylinders'},
   {'n': 1620, 'm': 1620, 's': 'bilayer'},
   {'n': 1620, 'm': 1620, 's': 'cylinders'},
   {'n': 1701, 'm': 1701, 's': 'bilayer'},
   {'n': 1701, 'm': 1701, 's': 'cylinders'},
   {'n': 1782, 'm': 1782, 's': 'bilayer'},
   {'n': 1782, 'm': 1782, 's': 'cylinders'},
   {'n': 1863, 'm': 1863, 's': 'bilayer'},
   {'n': 1863, 'm': 1863, 's': 'cylinders'},
   {'n': 1944, 'm': 1944, 's': 'bilayer'},
   {'n': 1944, 'm': 1944, 's': 'cylinders'}],
  'system': {'counterion': {'name': 'BR',
    'resname': 'BR',
    'nmolecules': 729,
    'reference_atom': {'name': 'BR'}},
   'surfactant': {'name': 'CTAB',
    'resname': 'CTAB',
    'nmolecules': 729,
    'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]},
    'head_atom': {'name': 'N1', 'index': 17},
    'tail_atom': {'name': 'C1', 'index': 1},
    'aggregates': {'shape': 'bilayer'},
    'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001],
     'radius': 11.460510481649582,
     'radius_connector_atom': 6.934818490775374},
    'head_group': {'diameter': 4.525691990874208}},
   'substrate': {'element': 'Au',
    'lattice_constant': 4.075,
    'approximate_measures': [200.0, 200.0, 200.0],
    'lmp': {'type': 11},
    'measures': [198.82074920012752, 199.633414036829, 197.62699714360895],
    'name': 'AUM',
    'resname': 'AUM',
    'reference_atom': {'name': 'AU'},
    'length': 198.82074920012752,
    'width': 199.633414036829,
    'height': 197.62699714360895,
    'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]],
    'natoms': 463680},
   'solvent': {'name': 'H2O',
    'resname': 'SOL',
    'reference_atom': {'name': 'OW'},
    'height': 180.0},
   'box': {'length': 198.82074920012752,
    'width': 199.633414036829,
    'height': 377.62699714360895}},
  'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'},
    'element_to_pdb_atom_name_mapping': {'Au': 'AU'},
    'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}},
   'packing': {'surfactant_substrate': {'tolerance': 1.5,
     'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617],
         [100.226, 100.354, 126.03802096329918]],
        'lower_constraint_plane': 105.37984599543711,
        'upper_constraint_plane': 122.27517496786207},
       {'bounding_box': [[-98.572, -99.281, 126.03802096329918],
         [100.226, 100.354, 150.45904192659833]],
        'lower_constraint_plane': 129.80086695873626,
        'upper_constraint_plane': 146.69619593116124}]}}},
   'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS',
    'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'},
    'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-49-886038/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'},
    'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-49-886038/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'}}},
  'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation',
  'creation_date': '2020-10-13 23:31:15.200230',
  'expiration_date': '2022-10-13 23:31:15.200230',
  'type': 'energy_file'},
 'compressed': True,
 'gfs_id': '5f8687378752d7b81fa747ea'}
In [130]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [131]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)
In [132]:
[ c for c in cursor]
Out[132]:
[{'_id': {'shape': 'bilayer', 'nmolecules': 972},
  'degeneracy': 1,
  'latest': '5f86967ffd2a730dccbbc7b8'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 567},
  'degeneracy': 1,
  'latest': '5f8692fb6b7f8f8ab3bbe5b5'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 243},
  'degeneracy': 1,
  'latest': '5f868b04beec446e55bb4f8c'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 1053},
  'degeneracy': 1,
  'latest': '5f86ac660bda12f287bbe0af'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 729},
  'degeneracy': 1,
  'latest': '5f86a860beec446e55bbae82'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 486},
  'degeneracy': 1,
  'latest': '5f86930cfd2a730dccbbbf8e'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 243},
  'degeneracy': 1,
  'latest': '5f868c31beec446e55bb57dc'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 324},
  'degeneracy': 1,
  'latest': '5f868b2f0bda12f287bb715d'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 162},
  'degeneracy': 1,
  'latest': '5f868c0afd2a730dccbb8c45'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 81},
  'degeneracy': 1,
  'latest': '5f868e628752d7b81fa771b2'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 810},
  'degeneracy': 1,
  'latest': '5f86a9bc0bda12f287bbd884'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 405},
  'degeneracy': 1,
  'latest': '5f8689366b7f8f8ab3bbda9a'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1296},
  'degeneracy': 1,
  'latest': '5f95a3e74e2af1e9d00ff6ea'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 972},
  'degeneracy': 1,
  'latest': '5f86d4fe8752d7b81fa78c57'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 162},
  'degeneracy': 1,
  'latest': '5f868cdbfd2a730dccbb946c'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 81},
  'degeneracy': 1,
  'latest': '5f868d1abeec446e55bb6136'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 648},
  'degeneracy': 1,
  'latest': '5f8688566b7f8f8ab3bbd204'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1053},
  'degeneracy': 1,
  'latest': '5f95a6654e2af1e9d00fff1e'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 891},
  'degeneracy': 1,
  'latest': '5f869ae58752d7b81fa7831f'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 810},
  'degeneracy': 1,
  'latest': '5f8687d38752d7b81fa75013'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 648},
  'degeneracy': 1,
  'latest': '5f86935c6b7f8f8ab3bbee25'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 567},
  'degeneracy': 1,
  'latest': '5f8687d26b7f8f8ab3bbc9df'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 324},
  'degeneracy': 1,
  'latest': '5f8689358752d7b81fa76087'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 729},
  'degeneracy': 1,
  'latest': '5f8687378752d7b81fa747ea'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 486},
  'degeneracy': 1,
  'latest': '5f8688578752d7b81fa7583f'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 405},
  'degeneracy': 1,
  'latest': '5f8688db0bda12f287bb68ea'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1944},
  'degeneracy': 1,
  'latest': '5f95951c7d270025bd0bc7ff'}]
In [136]:
res_list = []

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [*[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()
...........................
In [137]:
res_df.columns
Out[137]:
Index(['shape', 'nmolecules', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Box-X',
       'Box-Y', 'Box-Z', 'Volume', 'Density', 'pV', 'Enthalpy', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')
In [138]:
res_df_mi
Out[138]:
Time Bond U-B Proper Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) ... Coul-SR:rest-rest LJ-SR:rest-rest Coul-14:rest-rest LJ-14:rest-rest T-non-Substrate T-Substrate Lamb-non-Substrate Lamb-Substrate
shape nmolecules step
cylinders 810 0.0 0.0 16264.279297 111387.351562 47319.957031 983.418762 -901366.062500 -80354296.0 -9223811.0 ... -9568941.0 9.973058e+05 0.0 0.0 298.966431 0.905010 1.0 1.0
1.0 1.0 15515.659180 110481.304688 46982.023438 959.010559 -901346.687500 -83095416.0 -9230427.0 ... -9574447.0 9.963634e+05 0.0 0.0 297.083038 202.890442 1.0 1.0
2.0 2.0 15478.591797 110853.617188 47119.957031 972.424255 -900498.750000 -83534792.0 -9241975.0 ... -9586517.0 1.001856e+06 0.0 0.0 296.459137 124.773201 1.0 1.0
3.0 3.0 15364.682617 110848.882812 47307.242188 952.557922 -900446.187500 -83798248.0 -9236665.0 ... -9581678.0 9.992972e+05 0.0 0.0 295.193451 76.892738 1.0 1.0
4.0 4.0 15798.178711 111745.476562 47222.941406 1019.889893 -900592.562500 -83945688.0 -9253651.0 ... -9597190.0 1.005388e+06 0.0 0.0 295.129242 48.168221 1.0 1.0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
bilayer 81 96.0 96.0 1552.198853 10467.779297 4443.123535 85.521164 -90029.156250 -84102888.0 -10427179.0 ... -10460852.0 1.082824e+06 0.0 0.0 294.786072 3.053047 1.0 1.0
97.0 97.0 1494.216919 10431.462891 4498.831543 63.239334 -90148.429688 -84102632.0 -10427323.0 ... -10460611.0 1.083273e+06 0.0 0.0 295.064270 3.049385 1.0 1.0
98.0 98.0 1549.523193 10514.641602 4563.296387 92.133003 -90010.804688 -84108072.0 -10419038.0 ... -10452306.0 1.077700e+06 0.0 0.0 295.244629 3.042280 1.0 1.0
99.0 99.0 1509.640869 10488.359375 4554.408203 91.772423 -89981.796875 -84106640.0 -10422105.0 ... -10455053.0 1.078925e+06 0.0 0.0 294.980042 3.054925 1.0 1.0
100.0 100.0 1601.009888 10445.417969 4558.555176 61.140762 -90089.460938 -84100352.0 -10431736.0 ... -10465069.0 1.085661e+06 0.0 0.0 294.945251 3.049167 1.0 1.0

2727 rows × 87 columns

In [148]:
#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Volume',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        # grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        grp.plot('Time',y_quantity,ax=ax[position],legend=False,title=y_quantity)
        
fig.tight_layout()

Visualize trajectory

In [153]:
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration'},
    'metadata.type': 'mp4_file',
}
In [154]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[154]:
27
In [155]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [156]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        # obj_list.append(Video(filename=tmp.name)) 
        # obj_list.append(tmp.name)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')
...........................
In [157]:
for key, obj in obj_dict.items():
    print(key)
    display(obj)
('cylinders', 972)
('cylinders', 648)
('cylinders', 324)
('cylinders', 405)
('cylinders', 567)
('cylinders', 243)
('cylinders', 1053)
('cylinders', 729)
('cylinders', 486)
('cylinders', 162)
('cylinders', 81)
('cylinders', 810)
('bilayer', 162)
('bilayer', 81)
('bilayer', 648)
('bilayer', 1053)
('bilayer', 810)
('bilayer', 891)
('bilayer', 567)
('bilayer', 729)
('bilayer', 486)
('bilayer', 972)
('bilayer', 1944)
('bilayer', 243)
('bilayer', 324)
('bilayer', 405)
('bilayer', 1296)

Pre-evaluated RDF

Overview

In [158]:
query = { 
    "metadata.project": project_id,
    "metadata.type": {'$regex': '.*rdf$'},
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)
Out[158]:
243
In [159]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [160]:
res_df
Out[160]:
type earliest latest object_count
0 surfactant_tail_surfactant_tail_rdf 2020-10-13 23:31:57.808458 2020-10-13 23:31:58.860092 27
1 surfactant_head_surfactant_tail_rdf 2020-10-13 23:31:57.808455 2020-10-13 23:31:58.860090 27
2 surfactant_head_surfactant_head_rdf 2020-10-13 23:31:57.808453 2020-10-13 23:31:58.860088 27
3 substrate_surfactant_tail_rdf 2020-10-13 23:31:57.808451 2020-10-13 23:31:58.860086 27
4 substrate_surfactant_head_rdf 2020-10-13 23:31:57.808449 2020-10-13 23:31:58.860084 27
5 counterion_surfactant_tail_rdf 2020-10-13 23:31:57.808446 2020-10-13 23:31:58.860081 27
6 counterion_surfactant_head_rdf 2020-10-13 23:31:57.808444 2020-10-13 23:31:58.860079 27
7 counterion_substrate_rdf 2020-10-13 23:31:57.808442 2020-10-13 23:31:58.860076 27
8 counterion_counterion_rdf 2020-10-13 23:31:57.808440 2020-10-13 23:31:58.860074 27

Substrate - surfactant head RDF

In [161]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)
Out[161]:
27
In [162]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [167]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    # res_list.append(data)
    print('.',end='')
print('')
...........................
In [168]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Substrate - surfactant tail RDF

In [169]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)
Out[169]:
27
In [171]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}


aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
...........................
In [172]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
    
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant tail RDF

In [173]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)
Out[173]:
27
In [174]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}

aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
...........................
In [175]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['nmolecules']):
for pos, (nmolecules, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(nmolecules)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Relaxation analysis

Overview on objects in step

In [176]:
# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'}
}
In [177]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[177]:
383
In [178]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [179]:
res_df
Out[179]:
type name earliest latest object_count
0 mp4_file NaN 2020-10-13 23:31:57.921402 2020-10-13 23:31:58.157138 8
1 surfactant_tail_rmsd NaN 2020-10-13 23:31:57.921399 2020-10-13 23:31:58.157136 8
2 surfactant_head_rmsd NaN 2020-10-13 23:31:57.921397 2020-10-13 23:31:58.157133 8
3 substrate_rmsd NaN 2020-10-13 23:31:57.921395 2020-10-13 23:31:58.157131 8
4 counterion_rmsd NaN 2020-10-13 23:31:57.921392 2020-10-13 23:31:58.157128 8
5 surfactant_tail_surfactant_tail_rdf NaN 2020-10-13 23:31:57.921390 2020-10-13 23:31:58.157126 8
6 surfactant_head_surfactant_tail_rdf NaN 2020-10-13 23:31:57.921388 2020-10-13 23:31:58.157124 8
7 surfactant_head_surfactant_head_rdf NaN 2020-10-13 23:31:57.921386 2020-10-13 23:31:58.157122 8
8 substrate_surfactant_tail_rdf NaN 2020-10-13 23:31:57.921383 2020-10-13 23:31:58.157120 8
9 substrate_surfactant_head_rdf NaN 2020-10-13 23:31:57.921381 2020-10-13 23:31:58.157117 8
10 counterion_surfactant_tail_rdf NaN 2020-10-13 23:31:57.921379 2020-10-13 23:31:58.157115 8
11 counterion_surfactant_head_rdf NaN 2020-10-13 23:31:57.921376 2020-10-13 23:31:58.157113 8
12 counterion_substrate_rdf NaN 2020-10-13 23:31:57.921374 2020-10-13 23:31:58.157111 8
13 counterion_counterion_rdf NaN 2020-10-13 23:31:57.921372 2020-10-13 23:31:58.157108 8
14 index_file NaN 2020-10-13 23:31:57.921370 2020-10-13 23:31:58.157106 8
15 run_file NaN 2020-10-13 23:31:57.921367 2020-10-13 23:31:58.157104 8
16 topology_file NaN 2020-10-13 23:31:57.921365 2020-10-13 23:31:58.157102 8
17 data_file NaN 2020-10-13 23:31:57.921363 2020-10-13 23:31:58.157099 8
18 trajectory_file NaN 2020-10-13 23:31:57.921361 2020-10-13 23:31:58.157097 8
19 uncompressed_trajectory_file NaN 2020-10-13 23:31:57.921358 2020-10-13 23:31:58.157095 8
20 energy_file NaN 2020-10-13 23:31:57.814034 2020-10-13 23:31:58.865832 74
21 log_file NaN 2020-10-13 23:31:57.814031 2020-10-13 23:31:58.865829 74
22 checkpoint_file NaN 2020-10-13 23:31:57.814026 2020-10-13 23:31:58.865822 74
23 input relax_z_only.mdp None None 1

Global observables

In [194]:
query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)
Out[194]:
74
In [195]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [196]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)
In [197]:
res_list = []

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [*[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()
........................
In [198]:
res_df.columns
Out[198]:
Index(['shape', 'nmolecules', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Box-X',
       'Box-Y', 'Box-Z', 'Volume', 'Density', 'pV', 'Enthalpy', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')
In [199]:
res_df_mi
Out[199]:
Time Bond U-B Proper Dih. LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) ... Coul-SR:rest-rest LJ-SR:rest-rest Coul-14:rest-rest LJ-14:rest-rest T-non-Substrate T-Substrate Lamb-non-Substrate Lamb-Substrate
shape nmolecules step
bilayer 1944 0.0 0.0 39936.410156 289935.437500 118923.296875 3601.251709 -2.160646e+06 -84339680.0 -7723825.0 ... -8765402.0 9.768656e+05 0.0 0.0 296.816742 2.699537 1.0 1.0
1.0 1.0 39717.855469 286455.187500 122287.273438 3941.893066 -2.157035e+06 -84362672.0 -7709268.0 ... -8746435.0 9.679704e+05 0.0 0.0 298.772247 3.253741 1.0 1.0
2.0 2.0 39786.585938 282673.281250 121678.007812 4082.935791 -2.155238e+06 -84353024.0 -7711732.0 ... -8742852.0 9.703966e+05 0.0 0.0 298.515228 3.192918 1.0 1.0
3.0 3.0 39369.175781 280971.593750 122375.289062 4018.603760 -2.151787e+06 -84352016.0 -7717448.5 ... -8744444.0 9.695025e+05 0.0 0.0 297.532349 3.061393 1.0 1.0
4.0 4.0 39469.574219 280759.625000 121373.687500 3896.191895 -2.150179e+06 -84369072.0 -7709955.0 ... -8732732.0 9.560571e+05 0.0 0.0 297.537567 3.020302 1.0 1.0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
cylinders 729 2996.0 2996.0 13508.846680 93825.765625 42622.656250 470.645233 -7.913297e+05 -84183760.0 -9476877.0 ... -9773378.0 1.037954e+06 0.0 0.0 295.217285 2.965389 1.0 1.0
2997.0 2997.0 13331.565430 93072.046875 42518.507812 456.470490 -7.912239e+05 -84179056.0 -9484637.0 ... -9780930.0 1.042440e+06 0.0 0.0 295.269592 2.979168 1.0 1.0
2998.0 2998.0 13445.263672 93784.937500 42998.128906 444.005981 -7.910263e+05 -84184760.0 -9476664.0 ... -9773029.0 1.036592e+06 0.0 0.0 294.636444 2.977165 1.0 1.0
2999.0 2999.0 13504.045898 93202.882812 42822.843750 448.560028 -7.914327e+05 -84181440.0 -9472594.0 ... -9769012.0 1.038523e+06 0.0 0.0 294.838196 2.954648 1.0 1.0
3000.0 3000.0 13544.460938 93906.226562 42708.632812 456.516785 -7.915608e+05 -84181992.0 -9472383.0 ... -9770683.0 1.039171e+06 0.0 0.0 294.818451 2.965106 1.0 1.0

72024 rows × 87 columns

In [200]:
#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Volume',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        # grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        grp.plot('Time', y_quantity, ax=ax[position], legend=False, title=y_quantity)
        
fig.tight_layout()

Visualize trajectory

In [205]:
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'},
    'metadata.type': 'mp4_file',
}
In [206]:
# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)
Out[206]:
8
In [207]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [208]:
aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        # obj_list.append(Video(filename=tmp.name)) 
        # obj_list.append(tmp.name)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')
........
In [209]:
for key, obj in obj_dict.items():
    print(key)
    display(obj)
('cylinders', 648)
('cylinders', 486)
('cylinders', 567)
('cylinders', 243)
('bilayer', 567)
('bilayer', 324)
('bilayer', 648)
('bilayer', 729)

Pre-evaluated RDF

Overview

In [210]:
query = { 
    "metadata.project": project_id,
    "metadata.type": {'$regex': '.*rdf$'},
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[210]:
72
In [211]:
# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]
In [212]:
res_df
Out[212]:
type earliest latest object_count
0 surfactant_tail_surfactant_tail_rdf 2020-10-13 23:31:57.921390 2020-10-13 23:31:58.157126 8
1 surfactant_head_surfactant_tail_rdf 2020-10-13 23:31:57.921388 2020-10-13 23:31:58.157124 8
2 surfactant_head_surfactant_head_rdf 2020-10-13 23:31:57.921386 2020-10-13 23:31:58.157122 8
3 substrate_surfactant_tail_rdf 2020-10-13 23:31:57.921383 2020-10-13 23:31:58.157120 8
4 substrate_surfactant_head_rdf 2020-10-13 23:31:57.921381 2020-10-13 23:31:58.157117 8
5 counterion_surfactant_tail_rdf 2020-10-13 23:31:57.921379 2020-10-13 23:31:58.157115 8
6 counterion_surfactant_head_rdf 2020-10-13 23:31:57.921376 2020-10-13 23:31:58.157113 8
7 counterion_substrate_rdf 2020-10-13 23:31:57.921374 2020-10-13 23:31:58.157111 8
8 counterion_counterion_rdf 2020-10-13 23:31:57.921372 2020-10-13 23:31:58.157108 8

Substrate - surfactant head RDF

In [219]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[219]:
8
In [220]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [221]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [222]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Substrate - surfactant tail RDF

In [223]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[223]:
8
In [224]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}


aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [225]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
    
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant tail RDF

In [226]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[226]:
8
In [227]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}

aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [228]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['nmolecules']):
for pos, (nmolecules, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(nmolecules)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant head RDF

In [232]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[232]:
8
In [233]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [234]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [235]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [236]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant tail - surfactant tail RDF

In [241]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_tail_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[241]:
8
In [242]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [243]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [244]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [245]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - surfactant head RDF

In [249]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[249]:
8
In [250]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [251]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [252]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [253]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - surfactant tail RDF

In [254]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[254]:
8
In [255]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [256]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [257]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [258]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - substrate RDF

In [259]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_substrate_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[259]:
8
In [260]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [261]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [262]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [263]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - counterion RDF

In [269]:
query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_counterion_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)
Out[269]:
8
In [270]:
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())
In [271]:
res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')
........
In [272]:
n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [273]:
n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()
In [ ]: